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Here we present the Locus Reference Genomic LRG sequence format, which has been designed for the specifi c purpose of gene variant reporting.. The format builds on the successful Nationa

In 1993 Ernest Beutler wrote an eloquent letter to the

editor of the American Journal of Human Genetics

high-lighting the defi ciencies of the systems then used to describe DNA variants [1] Th at same year, the editor of

Human Mutation invited Arthur Beaudet and Lap-Chee

Tsui to produce a nomenclature for variants in genes and proteins [2] From these simple beginnings, the last 17 years have borne witness to the steady development of the nomenclature used to describe sequence variation that is now maintained under the auspices of the Human Genome Variation Society (HGVS) [3,4] To some, the present nomenclature may seem like an arcane art-form jealously guarded by zealots Th is may have been a valid criticism in the past, but advances in human genetics mean that embracing the nomenclature fully is now essential With the completion of the human genome sequence, the number of known variants has expanded dramatically, with many identifi ed as being associated with medical conditions For such variants, especially in the clinical setting, the need to describe them syste-matically is paramount [5-7]

Reference DNA sequences and their limitations

A crucial element of variant nomenclature is the refer-ence DNA sequrefer-ence with respect to which a variant is described Ideally, the sequence should have been submitted to a primary DNA sequence database and be identifi ed by an accession number and its version For the most part, this requirement is complied with nowadays, though the quality of the sequence data is sometimes

questionable For some genes, the de facto reference

sequences were established before the advent of high-throughput sequencing technologies Intron and inter-genic sequence data were often less reliable than those of the exons for these legacy sequences due to the defi ciency

of read-depth coupled with the lack of corroboration of the DNA sequence against a corresponding protein At the start of the millennium, recognizing the need for

Abstract

As our knowledge of the complexity of gene

architecture grows, and we increase our understanding

of the subtleties of gene expression, the process of

accurately describing disease-causing gene variants

has become increasingly problematic In part, this is

due to current reference DNA sequence formats that

do not fully meet present needs Here we present the

Locus Reference Genomic (LRG) sequence format,

which has been designed for the specifi c purpose

of gene variant reporting The format builds on

the successful National Center for Biotechnology

Information (NCBI) RefSeqGene project and provides

a single-fi le record containing a uniquely stable

reference DNA sequence along with all relevant

transcript and protein sequences essential to the

description of gene variants In principle, LRGs can

be created for any organism, not just human In

addition, we recognize the need to respect legacy

numbering systems for exons and amino acids and

the LRG format takes account of these We hope that

widespread adoption of LRGs - which will be created

and maintained by the NCBI and the European

Bioinformatics Institute (EBI) - along with consistent

use of the Human Genome Variation Society

(HGVS)-approved variant nomenclature will reduce errors in

the reporting of variants in the literature and improve

communication about variants aff ecting human health

Further information can be found on the LRG web site

(http://www.lrg-sequence.org)

Locus Reference Genomic sequences: an improved

basis for describing human DNA variants

Raymond Dalgleish1*, Paul Flicek2, Fiona Cunningham2, Alex Astashyn3, Raymond E Tully3, Glenn Proctor2, Yuan Chen2,

William M McLaren2, Pontus Larsson2, Brendan W Vaughan2, Christophe Béroud4, Glen Dobson5, Heikki Lehväslaiho6,

Peter EM Taschner7, Johan T den Dunnen7, Andrew Devereau5, Ewan Birney2, Anthony J Brookes1 and Donna R Maglott3

*Correspondence: raymond.dalgleish@le.ac.uk

1 Department of Genetics, University of Leicester, University Road, Leicester

LE1 7RH, United Kingdom

Full list of author information is available at the end of the article

© 2010 Dalgleish et al; licensee BioMed Central Ltd This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any

higher quality reference data, the National Center for

Bio-technology Information (NCBI) established a database of

curated non-redundant reference sequences of genomes,

transcripts and proteins known as RefSeq [8,9] Until

recently, most human genomic DNA sequences

represented in RefSeq have been of genomes rather than

individual genes Consequently, the reporting of variants

in genomic DNA coordinates using RefSeq genomic

contig sequences has been cumbersome, especially if the

gene of interest lies on the reverse strand For example,

the human COL1A1 gene is the reverse complement of

bases 13535609 to 13553152 in the RefSeq record

NT_010783.15 Beginning in 2007, RefSeq has been

extended to embrace reference sequences for individual

genes through the creation of RefSeqGene records [10]

Many authors still prefer to report intronic sequence

variants in terms of cDNA coordinates (for example,

c.2451+77C>T, or the now deprecated format,

IVS36+77C>T), even though the nomenclature to do so is

somewhat awkward However, the use of cDNA

coordi-nates is permitted with RefSeqGene reference sequences

In spite of these welcome developments, users of these

sequences must be aware of the update policies of public

sequence databases Th ere are two types of modifi cation

to a public sequence record: changes to the sequence, or

changes to the annotation or description of that

sequence Th e latter type of change is refl ected only by a

change to the modifi cation date of the record, and will be

changed if the gene symbol changes, citations associated

with the record change, or the position of features (such

as the coordinates of exons) within that sequence are

revised Th e former type of change - that is, to the

se-quence itself - results in the incrementing of the version

of the sequence For example, the sequence of the

desmo-glein 2 gene, DSG2, was revised from version

NG_007072.1 to version NG_007072.2 in December

2007 In May 2008, re-interpretation of the mRNA

coding regions of the sequence of NG_007072.2 resulted

in a change of version number for the corresponding

RefSeq mRNA record for DSG2 from NM_001943.2 to

NM_001943.3 though no change to the RefSeq protein

genomic DNA record and the RefSeq protein record both

retained the same version numbers as before, but the

RefSeq mRNA record version was incremented

Anec-dotal evidence, especially from journal editors, suggests

that these issues are poorly understood by researchers

who fail to mention the version number of reference

sequences that they have used as the basis for reporting

sequence variants Variant reports that do not clearly

defi ne the version of the used reference sequence might

have ambiguous interpretations

Failure to fully embrace the issues surrounding

version-ing of reference sequences can lead to inconsistency of

variant descriptions from one generation of patients to the next An individual testing positive for a given variant today may have children who, years later, wish to seek genetic counseling and be tested for that same variant To avoid any misunderstanding or confusion by the counselor and the staff of the diagnostic laboratory, it is essential that changes to reference DNA sequences are closely monitored by these parties to militate against the possibility of a change of description for the tested variant (see Box 1 for a hypothetical example)

Another limitation is that current reference sequences may not represent all transcripts that arise through the use of distinct transcription start sites, alternative splic-ing, or polyadenylation signals (Box 2) Currently, genomic reference sequences do not necessarily record all of the known mRNAs, focusing instead on information con-cern ing the single most abundant mRNA Ideally, a reference sequence for a gene would include all relevant spliced transcripts necessary for variant reporting, reducing the risk that an eff ect of the variant on an alternatively spliced transcript might be missed

A further limitation is that the present annotation scheme does not take account of well-established legacy

Box 1 Nomenclature problems because of reference sequence versioning

A clinical genetics centre treats Jenny, a patient with a family history of the RP10 form of autosomal dominant retinitis

pigmentosa caused by a variant in the IMPDH1 gene The

variant was initially found in her father some time ago and is described in a paper published just before he was diagnosed with the disease The paper cites the GenBank RefSeq mRNA record NM_000883 when describing the structure of the gene The variant is described using a nucleotide number from NM_000883 and a codon number from the translation product

of that transcript However, the version number of the GenBank record is not given in the paper and now, when the laboratory looks in GenBank (by following a hyperlink to NM_000883 given

in the online version of the paper) they fi nd that the current version is NM_000883.3, with a date stamp in March 2010 The exon structure of the gene was revised in 2003 and this resulted

in the base, codon and exon numberings being changed The variant reported in the literature is therefore no longer found at the expected location in the mRNA and protein sequences.

Laboratories specializing in this gene know that the numbering relative to the start codon has changed and recognize this as

a potential source of error Considerable eff ort is required to translate data in published papers and databases between diff erent versions of reference sequences to gather the information needed to analyze cases like Jenny’s This extra complexity means that the service may take longer and be more expensive than it otherwise might be Unfortunately,

new variants in the IMPDH1 gene are still being described in

the literature without specifying the version of the reference sequence.

numbering schemata that are in use at present, or have

been used in the past, to number features such as exons

or amino acids Th e globins and the collagens provide

excellent examples of legacy systems (Box 3) Ideally,

reference sequences would be annotated in a fashion that

would allow for verifi cation of variants reported using

either legacy or HGVS-compliant nomenclatures

To address these limitations, a meeting sponsored and

organized by the multi-institute European Union-funded

GEN2PHEN project [11] was held, with representatives

of GEN2PHEN (Genotype-To-Phenotype Databases

Project), European Bioinformatics Institute (EBI) [12]

and NCBI [13] in attendance, to discuss the specifi cation

for stable reference genomic DNA sequences better

suited to the task of reporting variants Th e participants

were geneticists, bioinformaticians, clinicians and

Locus-specifi c Database (LSDB) curators In advance of the

meeting, a survey was conducted by GEN2PHEN with

the help of the HGVS [14] to assess the views of the

curators of LSDBs

universally acceptable standard: a new specifi cation for

human genomic DNA reference sequences that would

address the shortcomings of non-standardized reporting

resulting from a variety of issues Th ese include the lack

of universally agreed genomic reference sequences for

some genes even though mRNA, expressed sequence tag

and genomic assembly records already exist Sometimes,

there are DNA sequence inconsistencies between existing

ad hoc genomic reference sequences (where no

RefSeqGene record has yet been created) and their NCBI

RefSeq mRNA sequence counterparts Inconsistent and

incomplete (and sometimes outdated and inappropriate)

annotation of existing ad hoc reference sequences and

Box 2 Genes with multiple spliced transcripts

Most human genes undergo alternative splicing, and perhaps

one of the most extreme examples is that of the calcitonin

gene (CALCA), which produces two distinct peptide-hormone

products: calcitonin (CT) in the thyroid gland and α-calcitonin

gene-related peptide (α-CGRP) in the brain [35] The two mature

peptides have no amino acid sequence in common and arise

from translation of alternatively spliced mRNAs CT and α-CGRP

are represented in RefSeq mRNA records NM_001033952 and

NM_001033953, respectively, for the CALCA gene The LRG record

LRG_13 has been created for this gene.

The INK4a/ARF multifunctional tumor-suppressor locus [36]

(CDKN2A) provides an additional example of the need to record

all clinically relevant transcripts The gene comprises four exons

whose transcripts are alternatively spliced and encode both the

p16 INK4a and p14 ARF tumor-suppressor proteins The unexpected

feature of this gene is that alternative fi rst exons used by the two

major transcripts result in the shared exon 2 being translated

in diff erent reading frames The LRG record LRG_11 has been

created for this gene.

Box 3 Legacy numbering schemata

The amino acid sequence of several human globin chains [37] was determined in the late 1950s and early 1960s by direct protein sequencing prior to the advent of gene cloning and DNA sequencing In these original sequences, the fi rst amino acid of the human α-, β- and δ-globins is valine and that of γ-globin is glycine However, HGVS nomenclature numbers the amino acids beginning with the methionine encoded by the initiation codon Consequently, the sickle-cell disease β-globin variant, in which glutamic acid is replaced by valine, should be reported as being at position 7, rather than 6, according to HGVS recommendations Indeed, this variant is still described in OMIM (Online Mendelian Inheritance in Man) [38] and in the HbVar database for hemoglobin variants thalassemia mutations [39,40]

in terms of the legacy amino acid numbering scheme.

Even though non-standard, the legacy numbering of the globin amino acids is well recognized by experts in the fi eld However, this is not true for newcomers or students who may blindly assume that standards are being applied and may become either completely lost or waste valuable time sorting out the problem The same is also true in the case of phosphoglycerate

kinase 1 (PGK, encoded by the PGK1 gene), where considerable

confusion has arisen from describing variants in relation to alterations to the known mature amino acid sequence [41] Again, the issue arises because PGK is one of the few enzymes in which variants were characterized at the amino acid level prior

to DNA sequencing being widely used.

The collagens also provide excellent examples of legacy numbering schemes Because of the lure of the characteristic triple-helical nature of the collagens, numbering of the amino acids was established decades ago with the fi rst glycine of the (Gly-X-Y)n-repeat region being designated as amino acid number

1 In addition, when the fi rst genomic DNA clones were isolated, exons were initially numbered in the 3’ to 5’ direction, a lack of full-length cDNA clones hampering the determination of the exact number of exons Consequently, the fi rst osteogenesis imperfecta variant that was characterized was reported as being in exon 1 of

the COL1A2 gene, which encodes the α2 chain of type I collagen

[42] In fact, the gene is now known to comprise 52 exons and the variant lies in exon 52 using conventional numbering However,

other exon-numbering anomalies remain The COL1A1 and

COL1A2 genes that encode the alpha chains of type I collagen

are evolutionarily related but COL1A1 has a single exon that corresponds to exons 33 and 34 of COL1A2 This single exon is

known as exon 33/34 [43] and the designation, which is more than 20 years old, is still widely used in the current literature.

A further issue is the discovery of additional exons in genes where

an exon-numbering scheme has already been established This

has resulted in the opioid receptor, mu 1 gene (OPRM) having

exons designated O, X and Y, with exons 3 and 5 divided into two and fi ve sub-regions, respectively [44], and the cystic fi brosis

transmembrane conductance regulator gene (CFTR) having exons

designated 6a, 6b, 14a, 14b, 17a and 17b [45].

missing annotation of clinically relevant transcripts is an

additional problem Present sequence record systems do

not provide support for legacy amino acid and exon

numbering schemes Finally, the new standard needed to

address the lack of understanding of the signifi cance of

‘versioning’ of sequence data

Th e principles guiding the discussions with respect to

the specifi cations for genomic reference sequences were

threefold First, the sequences need not represent real

alleles of genes: they can be composites that provide a

practical working framework for the reporting of

variants Second, research or diagnostic laboratories,

LSDB curators, mutation consortia, and so on that have a

direct interest in given genes will have the fi nal say in

defi ning the sequences and their annotation Th ird,

stability of the sequences, their core annotation, and their

identifi ers is essential to ensure consistency of variant

reporting over time frames of many decades

Th e agreed solution was the concept of an LRG (Locus

Reference Genomic) [15], which builds on the initial

ideas from NCBI for RefSeqGene LRGs will only be

created in response to demand from the community

which, in practice, is likely to be from LSDB curators or

from diagnostic laboratories LRGs are not restricted to

protein coding genes, but will be created for any region of

the genome within which sequence variation needs to be

recorded, including regulatory regions that encode

RNAs However, the mitochondrial genome is explicitly

excluded as its sequence (RefSeq NC_012920.1) and

variation is already managed by MitoMap [16] Th e LRG

system provides a genomic DNA sequence representation

of a single gene that is idealized, has a permanent ID

(with no versioning), and core content that never changes

(that is, nucleotide sequence, transcripts, exons, start and

stop codon positions) Th is core annotation will be

known as the ‘fi xed-annotation layer’ Although LRGs are

created for single genes, some might encompass all, or

part, of overlapping or adjacent genes, as currently

happens with RefSeqGene records Th e LEPRE1 (leucine

proline-enriched proteoglycan (leprecan) 1) LRG

(LRG_5) also includes part of the C1orf50 (chromosome

1 open reading frame 50) gene, which is encoded on the

opposite strand A separate LRG will be created for

C1orf50 if there is a request from the community.

Additional annotations, known as the

‘updatable-anno-tation layer’, that may change with time (each item

carrying its own date stamp) will provide ancillary

infor-ma tion about a gene Such annotations will include

details of additional transcripts and information for

mapping the LRG sequence onto genome assemblies (for

example, currently NCBI 36 and Genome Reference

Consortium Human (GRCh) 37) as well as

cross-referencing of features in the fi xed-annotation layer to

legacy coordinate systems

More than one LRG can be created for a region of interest, should the need arise If essential changes to any

of the core sequence data are required, such as the need

to include a newly discovered upstream exon, a new LRG record will be generated with a new ID Sequence variants may be validly expressed with reference to the original LRG (which will not be retired) or to its replacement An LRG provides a stable sequence and numbering system against which samples can be com-pared and variation be reported Although annotation is provided, the LRG is not intended to aggregate and report all known variants

Variation will be reported using HGVS nomenclature [4] and the use of an LRG as the reference standard supports all coordinate systems: using genomic DNA coordinates, LRG_1:g.8463G>C is equivalent to NG_007400.1:g.8463G>C; using coding DNA coordi nates, LRG_1t1:c.572G>C is equivalent to NM_000088.3:c.572G>C; using protein coordinates, LRG_1p1:p.Gly191Ala is

equi-va lent to NP_000079.2:p.Gly191Ala As a feature of the LRG project, the coordinate system of a RefSeqGene that matches an LRG will be so indicated and will not be changed

LRGs aff ord three key improvements in comparison with RefSeqGene records LRGs provide a ‘one-stop’ sequence record for a gene (with a single accession number) comprising sequences for the gene itself, all of the transcripts essential for the reporting of sequence variants, and the corresponding predicted proteins translated from each transcript Th e locking of the sequences within the LRG means that ‘version-control’ is not an issue in the reporting of sequence variants No sequence (genomic DNA, mRNA or protein) within the

fi xed layer will ever be changed or removed Finally, the inclusion of the necessary data facilitates reference to features, such as exons or amino acids, using legacy numbering or naming schemes

Implementing LRGs

NCBI continues to identify genes of clinical interest and create RefSeqGene records [10] In March 2010, RefSeqGene sequences were available for more than 2,800 genes and many of these are already in use in LSDBs To ease the transition towards the use of LRGs, they will be created from any pre-existing RefSeqGene record Th e goal is to maximize the similarities When a RefSeqGene record is assigned an LRG accession, it means that the sequence, transcripts, proteins and exons are identical for that version of the RefSeqGene and the LRG In other words, it will make no diff erence if variants are reported in LRG or RefSeqGene coordinates

XML was chosen for exchanging and storing LRGs because of its ease of extensibility and validation as well

as its natural hierarchical structure, which lends itself

well to the nature of the information in LRGs Th ere are

numerous existing programmatic tools for defi ning,

vali dat ing, parsing and transforming XML Th e XML

schema is defi ned using Relax NG [17] and is available

on the EBI FTP site [18] XSLT style-sheets have been

produced that will transform the XML into more

user-friendly HTML or plain text Th ese are also available

from the FTP site

Th e LRG fi le has separate XML sections for the fi

xed-annotation and updatable-xed-annotation layers Within the

tags for the fi xed layer are the genomic sequence and

transcripts that defi ne the LRG, together with the

corresponding cDNA sequence, amino acid sequence

and exon coordinate markup Th e updatable section

con-tains database cross-references, reports of any

over-lapping LRGs, detailed information on how the LRG

maps to the human genome assembly and information to

map systematic exon and amino acid coordinates onto

their legacy equivalents

LRGs will be compiled and maintained by the NCBI

and EBI Th is will ensure that the data contained in LRGs

are accurate and consistent with data in other existing

sequence records Th e key involvement of these

organiza-tions means that the LRG format has an assured

long-term future on which users can rely beyond the end of

the GEN2PHEN project

Downloading and viewing LRGs

Th e LRG website [15] provides access to existing LRG

records and mechanisms for requesting new LRGs Before

making a request, it is advisable that users familiarize

themselves with the complete LRG specifi cation [19],

which is available on the LRG website, and feedback is

invited on any aspect of the specifi cation

To facilitate viewing of LRGs, Ensembl [20,21] has

adapted their browser NCBI supports displays of LRG

sequences and reported variants using client software

(NCBI Genome Workbench [22]) and the graphical

se-quence viewer [23] Use of these tools facilitates

integra-tion of LRG data variant data in dbSNP (NCBI Database

of Genetic Variation) [24,25] Th e NGRL Universal

Browser (National Genetics Reference Laboratory,

Man-chester;) already provides a graphical view of LRGs [26]

with the ability, for some genes, to display tracks linked

to dbSNP and to appropriate LSDBs

A major issue with variant curation is how DNA

sequences might be visualized to make the process

simpler and less prone to error Journal editors and

referees are well aware of the frequency with which

authors report variants erroneously Ideally, a browser

will be developed that will integrate fully with the

commonly used LSDB systems, such as LOVD (Leiden

Open Variation Database) [27,28], UMD (Universal

Mutation Database) [29,30] and MUTbase (Maintenance

and Analysis of Mutation Databases on the World Wide Web) [31,32], allowing curators and submitters to auto-matically generate standards-compliant variant descrip-tions using the LRG sequences as a reporting reference standard

Tools such as Mutalyzer [33,34], both in its standalone form and through the API used by the LOVD variant database system, have made the process of correctly naming variants relative to all annotated transcripts and protein isoforms much simpler, but more sophisticated variant-visualization systems would be a welcome development Just as with Mutalyzer, such systems would parse the annotated features of reference DNA sequences

to provide the necessary visual cues to help generate an HGVS-nomenclature-compliant description of any variant Ideally, such a system would incorporate cross-checking with legacy numbering systems To achieve this, a robust and comprehensive feature-annotation scheme with a controlled vocabulary will be essential

Th e LRG specifi cation does not specifi cally entail the produc tion of a dedicated sequence browser, but produ-cing one that uses LRG sequences would facilitate the successful adoption of LRGs To this end, the LRG XML schema is fully open and has version control, allowing any party, commercial or public, to develop visualization tools

Closing remarks

Th e LRG specifi cation is the culmination of considerable debate among those participating in the project and has also been fashioned by the advice of external com men-tators Most of the proposals have been accepted readily, but two in particular have been controversial Th e fi rst is the proposal to allow addition of transcripts to the fi xed-annotation layer Th e argument is that this amounts to versioning and does not solve the existing version problem Versioning is an issue with traditional reference sequence records because the actual sequences diff er from version to version for records with the same accession number In the fi xed-annotation layer of the LRG, the sequence data for the genomic DNA, the transcripts and their translation products will never be changed or removed Consequently, a variant description such as LRG_13:g.8290C>A will always remain valid and will not be subject to misinterpretation

Likewise, the proposal to allow more than one LRG for the same gene region has also provoked similar argu-ments about versioning If it is no longer possible to describe a sequence variant in terms of an existing LRG,

it might be necessary to create a totally new LRG with a uniquely diff erent number (for example, LRG_1275 instead of the existing LRG_89) Th e original LRG will not be ‘retired’ and it will remain valid to describe variants with respect to that sequence record Creation of

additional LRGs for an existing gene or genomic region

will only be considered in the most exceptional

circum-stances and each will be cross-referenced with the other

in the updatable annotation layer

Finally, queries have been raised about the ability of

LRGs to support the reporting of copy number variation

(CNV) LRGs are no less well suited to the task of CNV

description than existing reference sequence records

Requests will be considered for the creation of a new

LRG representing a particular allele with respect to CNV

and we will work with the requesting party to achieve the

best practicable solution to represent the allele Again,

this will only be considered in the most exceptional

circumstances Th e issues that have been raised during

the development of the LRG specifi cation are the subject

of a frequently asked questions (FAQs) page, accessible

from the LRG home page

In the absence of any proposals of alternative solutions

to deal with these issues, we feel that LRGs provide a

pragmatic solution to the needs of LSDBs and clinical

laboratories with respect to reporting sequence variants

in a stable fashion

LRG timeline

Initial discussion of the need for improved reference

sequences suited to the task of curation of variants in

LSDBs took place at the fi rst general assembly meeting of

the GEN2PHEN project in January 2008 Immediately

following that meeting, a survey was distributed to LSDB

curators through the HGVS and the results were analyzed

in March 2008 In April 2008, a two-day workshop was

held at EBI to formulate the specifi cation of an improved

reference sequence that is now known as Locus Reference

Genomic (LRG) Creation of the formal LRG specifi cation

began in May 2008 and several versions were produced in

response to internal discussion and to feedback elicited

through the HGVS Th e current version (version 12) was

agreed in June 2009

Creation and revision of the LRG XML schema began

in March 2009 (currently at version 1.6) and the fi rst LRG

records were created in June 2009 At present, LRGs have

been fi nalized for ten genes and a further four await fi nal

approval Requests have been received for approximately

90 additional genes and these are currently in production

We invite enquiries concerning the creation of additional

LRGs

Availability

Access to further information and to LRG sequence

records is available at [15] A search facility is provided

and there is a link to frequently asked questions (FAQs)

Specifi c links are provided to request technical support,

to request the creation of new LRGs and to allow

feedback on the LRG specifi cation

Abbreviations

CNV: copy number variation; EBI: European Bioinformatics Institute;

GEN2PHEN: Genotype-To-Phenotype Databases Project; HGVS: Human Genome Variation Society; LOVD: Leiden Open Variation Database; LRG: Locus Reference Genomic; LSDB: Locus-specifi c Database; NCBI: National Center for Biotechnology Information.

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

The manuscript was drafted by RD with contributions from FC, GP and AD The manuscript was edited by RD, PF, FC, CB, HL, PEMT, JTdD, AD and DRM

RD, PF, CB, HL, PEMT, JTdD, EB, AJB and DRM participated in the conceptual basis and design specifi cation of LRGs AD gathered and represented the views of a group of potential users and developed an illustrative example of the requirement for LRGs GP and FC defi ned and implemented a format for LRG fi les PF, FC and DRM coordinated implementation of the LRG informatics infrastructure AA, RET, WMM, YC, and PL implemented the software and infrastructure for the project GD developed the NGRL LRG browser PEMT and JTdD tested the LRG format for compatibility with existing software tools BWV designed and implemented the LRG website RD wrote the FAQs on the LRG website.

Acknowledgements

We are grateful for the help of the Human Genome Variation Society in distributing the survey that was used in the initial development of the LRG specifi cation We are also grateful to those who responded to the survey and those who provided feedback on drafts of the specifi cation The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 - the GEN2PHEN project.

Author details

1 Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom 2 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom 3 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA 4 INSERM, U827, Montpellier, F-34000, France 5 NGRL Manchester, Genetic Medicine, 6th Floor, St Mary’s Hospital, Oxford Road, Manchester, M13 9WL, United Kingdom

6 Computational Bioscience Research Center, King Abdullah University

of Science and Technology, P.O Box 55455, Jeddah 21534, Saudi Arabia

7 Department of Human Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Received: 11 January 2010 Revised: 31 March 2010 Accepted: 15 April 2010 Published: 15 April 2010

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doi:10.1186/gm145

Cite this article as: Dalgleish R, et al.: Locus Reference Genomic sequences:

an improved basis for describing human DNA variants Genome Medicine

2010, 2:24.